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add SAMFileHeader #2323

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add SAMFileHeader #2323

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12 changes: 10 additions & 2 deletions adam-core/src/main/scala/org/bdgenomics/adam/ds/read/AnySAMOutFormatter.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -24,14 +24,16 @@ import org.bdgenomics.adam.ds.OutFormatter
import org.bdgenomics.formats.avro.Alignment
import scala.annotation.tailrec
import scala.collection.mutable.ListBuffer
import java.io.{ BufferedReader, InputStreamReader }
import org.bdgenomics.adam.ds._

/**
* An OutFormatter that automatically infers whether the piped input is SAM or
* BAM. Autodetecting streamed CRAM is not currently supported.
*/
case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[Alignment] {
case class AnySAMOutFormatter(stringency: ValidationStringency, header: SAMFileHeader) extends OutFormatter[Alignment] {

def this() = this(ValidationStringency.STRICT)
def this() = this(ValidationStringency.STRICT, new SAMFileHeader())

/**
* Reads alignments from an input stream. Autodetects SAM/BAM format.
Expand All @@ -46,6 +48,12 @@ case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutForma
.validationStringency(stringency)
.open(SamInputResource.of(is))

//copy reader header
val r_header = reader.getFileHeader()
header.setSequenceDictionary(r_header.getSequenceDictionary())
header.setReadGroups(r_header.getReadGroups())
header.setProgramRecords(r_header.getProgramRecords())

SAMIteratorConverter(reader)
}
}
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